Nearly three months after superstorm Sandy inundated their house with five feet of water, retirees Brian and Dorothy Beebe went to the town hall here, clutching a survey of their home stuffed into a brown envelope, eager to repair their split-level home along New Jersey's shore.

When they left, their best-laid plans – for their home, as well as for their life going forward – had been thrown into doubt. At town hall, clerks told them they may have to elevate their house as high as 11 feet above sea level on cinderblock walls. For a small house, that could cost $30,000. For a larger, more complex structure, as much as $100,000.

"It means we take out a mortgage on our retirement," says Ms. Beebe, who left with instructions to get an estimate and apply for federal assistance.

It's a frequent scene in Toms River and other battered New Jersey towns. Before Sandy arrived, the Federal Emergency Management Agency (FEMA) began redrawing New Jersey's flood maps to define which houses were at high risk as sea levels rise in connection with climate change. Now, in Sandy's wake, the potential costs of those calculations are hitting home for the Beebes and others.

Complicating matters is Congress's decision in July to end subsidies for federal flood insurance. Taken as a whole, it is a cautionary tale for the country, as many Americans – perhaps for the first time – discover how climate change can hit their pocketbooks.

Zoning official Bernard Mackle has worked in Toms River for 25 years, but he calls this "a new challenge." For his part, Mr. Mackle doesn't know if Sandy is related to climate change. Scientists point to overwhelming evidence that the world is getting warmer, and this has resulted in warmer oceans that fuel more extreme weather, as well as rising sea levels, which threatens coastal areas.

"If superstorm Sandy was in some way related to global warming, we are feeling the effects of it," he says as he reads through dozens of flood-related e-mails.

His more immediate concern, however, is how to deal with the new zoning codes. "We have to address how to impose the new codes that require homes to be lifted," he adds.

The new codes are needed in a time of changing climate, scientists say.

"You can't attribute Sandy to increased ocean temperatures, but the increased intensity of the storm can be attributed to a warmer ocean," says Kenneth Miller, an earth scientist at Rutgers University in New Jersey. Homeowners who do not elevate their houses "are rolling loaded dice for extreme events."

But imposing the new codes during storm cleanup has proved chaotic. Toms River is home to 95,000 people. Fifteen thousand homes were damaged or destroyed in the storm, nearly half the town's housing stock and a substantial portion of the 72,000 homes and businesses that were hit in New Jersey.

Jeannie and Gabrielle Kanterezhi-Gatto were desperate to move back into their home. The couple and their two children have lived with another family since Sandy soaked their one-story home two blocks from the water's edge. They paid a contractor to begin tearing down moldy walls and rewiring electricity, only to learn that their home would be too low, according to the new maps.

Jeanniewas close to tears as she left the community development office with her family.

"The town is saying, 'If you don't elevate your home, there will be higher flood insurance,' " she says. "Now we don't know what to do. We can't afford to raise the home. Where am I supposed to come up with this money?"

Her partner is a mental-health counselor, but the limbo is testing Jeannie's limits. It is difficult to be a guest for more than two months, she says. Also, the storm destroyed the second family car, which makes it hard to get around. She would love to just leave Toms River and start fresh – but she wonders who would buy a moldy home that needs to be hoisted up on pilings.

Mackle of the zoning office worries about residents like the Kanterezhi-Gattos.

"Officials in Louisiana towns that were hit by Katrina are dealing with that issue," he says. "If you don't get people and businesses back in their homes quickly, they don't come back. It was a real problem for people in the Gulf, and it could be here."

FEMA officials have heard complaints about affordability. But the government can no longer pay for the floods in coastal towns without raising rates.

"We want people to rebuild safer, smarter and more resilient," says Bill McDonnell, a FEMA official working in New Jersey. "The last thing we want them to do is to rebuild at same elevation they are now and have this happen again. If communities choose to start rebuilding at the old flood elevation, there are consequences."

The new maps – which Mackle has pinned to the wall in his office's reception room – are only preliminary. FEMA will publish official maps in the summer, and they will be subject to a three-month review period. Mr. McDonnell said FEMA released the early versions to give storm victims more information as they draw up their repair plans.

Mackle says FEMA officials have met with him and his colleagues to explain the maps and how the government can help offset the cost of compliance.

"FEMA has made it clear to me that they want to be helpful," Mackle says.

But whatever the final flood maps may be, they will fundamentally change the geography and prices of the reconstructed Toms River, Mackle says. Home buyers will judge a house not only for its views and proximity to the water, but also for its elevation and flood-insurance premiums.

For the Beebes, superstorm Sandy has soaked their retirement dream. They planned to spend their golden years sitting on their front porch, smelling the fresh water a street away and taking their boat out for pleasure rides on Silver Bay. Now that dream is deferred.

"We always lived on the East Coast," Ms. Beebe says. "We are happy here. We'll deal with it and move on."